In 2369, Keiko was involved in a shuttlecraft and transporter accident that resulted in her body being returned to that of her childhood self. A cure was eventually found to restore her to her adult form. (TNGepisode: "Rascals")

Later in 2369, Miles transferred to StarbaseDeep Space 9 and Keiko and the family went with him. With little use for a botanist, Keiko opened a school on the station. Later that year the school became the subject of a dispute over how the children, Federation and Bajoran, were being taught; some Bajorans taking offense at the Bajoran wormhole being explained as a scientific anomaly rather than for its theological value to the Bajoran people. This dispute eventually resulted in the school being bombed, fortunately when no one was in attendance. (DS9episodes: "Emissary", "A Man Alone", "In the Hands of the Prophets")

The next year Keiko was still wary of upsetting the Bajoran faith and was careful to make sure her students were mindful and respectful of each other's diverse beliefs. As she was trying to explain the Vulcan idiom of the IDIC to a Tellarite student a lost baby Horta burrowed into the class, inciting panic. Whilst the students fled Molly starting feeding the Horta a computer which seemed to keep it satisfied for a time, Keiko followed her daughter's example to keep the Horta happy. (DS9novel: Devil in the Sky)

The following year Keiko became pregnant with her and Miles's second child. However, after she was injured in a shuttle accident, the fetus had to be transplanted into the womb of Kira Nerys in order to save Keiko's and the child's life. The baby, Kirayoshi, was born the following year on DS9. (DS9episodes: "Accession", "Body Parts", "The Begotten")

In early December, shortly after the O'Briens relocated to Cardassia, Keiko was amongst a group of hostages taken by representatives of the Cardassian group calling themselves the True Way, who were attempting to destabilize the fledgling government of Alon Ghemor. The situation was brought to a peaceful conclusion and Keiko continued her work on Cardassia. (DS9novel: Cardassia: The Lotus Flower)

In 2378, while on Cardassia Miles was approached by the now-adult Rugal Pa'Dar - a Cardassian boy the O'Briens had hosted in 2369. Pa'Dar, who wished to become a Federation citizen and formally adopt the human ophan Hulya Kiliç, would ask Miles and Keiko how to go about this. It was decided he should travel to Earth and formally apply there. Keiko would accompany Rugal and Hulya, accompany them to the Cardassian Embassy on Earth and speak at Rugal's citizenship trial. (DS9novel: The Never-Ending Sacrifice)

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